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Plants can be primed to survive the exposure to a severe heat stress (HS) by prior exposure to a mild HS. The information about the priming stimulus is maintained by the plant for several days. This maintenance of acquired thermotolerance, or HS memory, is genetically separable from the acquisition of thermotolerance itself and several specific regulatory factors have been identified in recent years.
On the molecular level, HS memory correlates with two types of transcriptional memory, type I and type II, that characterize a partially overlapping subset of HS-inducible genes. Type I transcriptional memory or sustained induction refers to the sustained transcriptional induction above non-stressed expression levels of a gene for a prolonged time period after the end of the stress exposure. Type II transcriptional memory refers to an altered transcriptional response of a gene after repeated exposure to a stress of similar duration and intensity. In particular, enhanced re-induction refers to a transcriptional pattern in which a gene is induced to a significantly higher degree after the second stress exposure than after the first.
This thesis describes the functional characterization of a novel positive transcriptional regulator of type I transcriptional memory, the heat shock transcription factor HSFA3, and compares it to HSFA2, a known positive regulator of type I and type II transcriptional memory. It investigates type I transcriptional memory and its dependence on HSFA2 and HSFA3 for the first time on a genome-wide level, and gives insight on the formation of heteromeric HSF complexes in response to HS. This thesis confirms the tight correlation between transcriptional memory and H3K4 hyper-methylation, reported here in a case study that aimed to reduce H3K4 hyper-methylation of the type II transcriptional memory gene APX2 by CRISPR/dCas9-mediated epigenome editing. Finally, this thesis gives insight into the requirements for a heat shock transcription factor to function as a positive regulator of transcriptional memory, both in terms of its expression profile and protein abundance after HS and the contribution of individual functional domains.
In summary, this thesis contributes to a more detailed understanding of the molecular processes underlying transcriptional memory and therefore HS memory, in Arabidopsis thaliana.
Epigenetische Mechanismen spielen eine entscheidende Rolle bei der Pathogenese von Colitis ulcerosa (CU). Ihr Einfluss auf das beobachtete Ungleichgewicht zwischen pro- und anti-inflammatorischen Cytokinen ist hingegen weitgehend unerforscht. Einige der wichtigsten immunmodulatorischen Cytokine sind die Mitglieder der heterodimeren Interleukin- (IL-) 12-Familie, die durch das Kombinieren einer der drei α-Ketten (IL-12p35, IL-27p28, IL-23p19) mit den ß-Untereinheiten IL-12p40 oder EBI3 (Epstein-Barr Virus-induziertes Gen 3) charakterisiert sind. IL-35 (IL-12p35/EBI3) spielt eine bedeutende anti-inflammatorische Rolle bei verschiedenen Erkrankungen, wohingegen seine Level bei chronischen Entzündungen erniedrigt sind. Eine mögliche Ursache könnte eine transkriptionelle Stilllegung über epigenetische Modifikationen sein. Tatsächlich konnte durch die Stimulation mit dem DNA-Methyltransferase-Inhibitor (DNMTi) Decitabin (DAC; Dacogen®) eine Induktion von EBI3 in humanen Epithelzellen aus gesundem Colon (HCEC) erreicht werden, die als Modell für ein lokales Entzündungsgeschehen dienten. Diese Regulation über DNA-Methylierung konnte in weiteren humanen Zellen unterschiedlichen Ursprungs sowie durch Stimulation von HCEC-Zellen mit zwei weiteren DNMTi, dem Cytosin-Analogon Azacytidin (AZA; Vidaza®) und dem natürlich vorkommenden, epigenetisch wirksamen Polyphenol Epigallocatechingallat (EGCG), verifiziert werden. Die kombinierte Inkubation mit Tumor-Nekrose-Faktor α (TNFα) resultierte jeweils in einer über-additiven Induktion von EBI3.
Weiterführende Untersuchungen zeigten, dass TNFα trotz Beeinflussung der epigenetischen DNMT- und Ten-eleven Translocation- (TET-) Enzyme keinen Einfluss auf die globalen Methylierungs- oder Hydroxymethylierungslevel hatte, jedoch eine genspezifische DNA-Hypomethylierung im EBI3-Promotor induzierte. Durch Nutzung verschiedener Inhibitoren konnte darüber hinaus nachgewiesen werden, dass der beobachtete synergistische Effekt der gemeinsamen DAC und TNFα-Stimulation hauptsächlich über NFκB (Nuclear factor “kappa-light-chain-enhancer” of activated B-cells) vermittelt wird. Ein Teil verläuft dabei über p38 MAPK (mitogen-activated protein kinases), während die JNK- (c-Jun N-terminale Kinasen-) und ERK- (extracellular-signal-regulated kinases) Signalwege keine Rolle spielen.
In der vorliegenden Arbeit wurde zudem gezeigt, dass die DNA-Hypomethylierung während eines entzündlichen Zustandes auch in einer erhöhten EBI3-Proteinexpression resultiert. Die Höhe der immunologisch detektierten Banden wies auf eine Dimerbildung sowohl im Zelllysat als auch im Überstand hin. Humane Colonepithelzellen sind demnach in der Lage, Cytokine zu bilden und zu sezernieren, was die Bedeutung von Nicht-Immunzellen bei der lokalen Immunantwort unterstreicht. Mittels Genexpressionsanalysen wurden IL-12p35 und IL-23p19 als mögliche Bindungspartner identifiziert. Aufgrund kreuzreaktiver Antikörper ist ein direkter Nachweis der EBI3-Dimere derzeit nicht möglich. Die stattdessen genutzte Kombination verschiedener Methoden dient als geeigneter Ersatz für die problematischen Antikörper-basierten Analysen wie Immunpräzipitation oder ELISA. Durch molekularbiologische, immunologische und massenspektrometrische Methoden konnte IL-35 identifiziert werden, während IL-39 (IL-23p19/EBI3) nicht detektiert wurde. Dies ist in Einklang mit den Erkenntnissen mehrerer Forschungsgruppen, die eine Bildung des nativen humanen Dimers aus IL-23p19 und EBI3 bezweifeln. Des Weiteren wurde die biologische Aktivität des behandlungsinduzierten IL 35-Proteins durch einen Funktionsassay nachgewiesen.
Neben einer DNMTi-bedingten transkriptionellen Aktivierung konnte eine Regulation von EBI3 über Histonacetylierungen gezeigt werden. Der EBI3-induzierende Effekt des Histondeacetylasen-Inhibitors (HDACi) Trichostatin A (TSA) wurde durch SAHA (suberoylanilide hydroxamic acid (Vorinostat; Zolinza®)) verifiziert. Ähnlich zu der Stimulation mit den hypomethylierenden Substanzen wurde ein synergistischer Effekt bei paralleler Inkubation mit TNFα beobachtet, der in einer gesteigerten Bildung des EBI3-Proteins resultierte.
Um die Befunde in einem komplexeren in vivo-Modell zu untersuchen, wurde eine chronische Colitis in Ebi3-defizienten Mäusen und dem dazugehörigen Wildtypstamm C57BL/6 durch zyklische Applikation von Natriumdextransulfat (Dextran sodium sulfate (DSS)) induziert. Der Vergleich klinischer Parameter wie Mortalitätsrate und Körper- sowie Milzgewicht wies bei Abwesenheit von Ebi3 signifikant stärkere colitische Symptome auf. Dies bestätigte die zentrale Rolle von Ebi3 in der Colitisentwicklung und deutete auf eine bevorzugte Bildung des anti-inflammatorisch wirkenden IL-35 statt des pro-inflammatorischen IL-39 in den Wildtyptieren hin. Durch zusätzliche therapeutische Behandlung der C57BL/6-Mäuse nach der DSS-Gabe konnte die in der Literatur beschriebene positive Wirkung von SAHA auf die Colitismanifestation bestätigt werden. Im Gegensatz dazu war der HDACi in den Ebi3-defizienten Tieren nicht in der Lage, die colitischen Parameter zu verbessern beziehungsweise verschlimmerte den Krankheitsphänotyp. Expressionsanalysen von Up- und Downstream-Target-Genen lieferten weitere Hinweise darauf, dass bei Anwesenheit von Ebi3 IL-35 statt IL-39 gebildet wird, was in Einklang mit den in vitro-Untersuchungen steht.
Die vorliegende Arbeit konnte durch den Vergleich der C57BL/6-Mäuse mit den Ebi3-defizienten Tieren neue Erkenntnisse über die Wirkungsweise von SAHA erbringen. Histonacetylierende Bedingungen verbessern colitische Symptome über einen Mechanismus, der die epigenetische Induktion von Ebi3 mit nachfolgender IL-35-Bildung involviert. Durch Kooperation der epigenetischen Mechanismen Hypomethylierung und Histonacetylierung wurde der stärkste Effekt auf die EBI3-Induktion bewirkt.
Insgesamt konnte in der vorliegenden Arbeit durch in vitro- und in vivo-Analysen die epigenetische und NFκB-vermittelte Induktion von EBI3 über DNA-Demethylierung und Histonacetylierung mit nachfolgender IL-35-Bildung und –Sezernierung nachgewiesen werden. Da IL-35 in der Lage ist, colitische Symptome zu mildern, stellt die epigenetische Reaktivierbarkeit von EBI3 durch DNMTi und HDACi eine vielversprechende Alternative für die derzeit genutzten, oft nicht oder nur kurzfristig wirksamen Therapien bei der Behandlung einer CU dar. Einer übermäßigen Immunantwort während schubweiser entzündlicher Phasen könnte entgegengewirkt und Komplikationen wie die Bildung Colitis-assoziierter Karzinome verhindert werden.
As of late, epidemiological studies have highlighted a strong association of dairy intake with lower disease risk, and similarly with an increased amount of odd-chain fatty acids (OCFA). While the OCFA also demonstrate inverse associations with disease incidence, the direct dietary sources and mode of action of the OCFA remain poorly understood.
The overall aim of this thesis was to determine the impact of two main fractions of dairy, milk fat and milk protein, on OCFA levels and their influence on health outcomes under high-fat (HF) diet conditions. Both fractions represent viable sources of OCFA, as milk fats contain a significant amount of OCFA and milk proteins are high in branched chain amino acids (BCAA), namely valine (Val) and isoleucine (Ile), which can produce propionyl-CoA (Pr-CoA), a precursor for endogenous OCFA synthesis, while leucine (Leu) does not. Additionally, this project sought to clarify the specific metabolic effects of the OCFA heptadecanoic acid (C17:0).
Both short-term and long-term feeding studies were performed using male C57BL/6JRj mice fed HF diets supplemented with milk fat or C17:0, as well as milk protein or individual BCAA (Val; Leu) to determine their influences on OCFA and metabolic health. Short-term feeding revealed that both milk fractions induce OCFA in vivo, and the increases elicited by milk protein could be, in part, explained by Val intake. In vitro studies using primary hepatocytes further showed an induction of OCFA after Val treatment via de novo lipogenesis and increased α-oxidation. In the long-term studies, both milk fat and milk protein increased hepatic and circulating OCFA levels; however, only milk protein elicited protective effects on adiposity and hepatic fat accumulation—likely mediated by the anti-obesogenic effects of an increased Leu intake. In contrast, Val feeding did not increase OCFA levels nor improve obesity, but rather resulted in glucotoxicity-induced insulin resistance in skeletal muscle mediated by its metabolite 3-hydroxyisobutyrate (3-HIB). Finally, while OCFA levels correlated with improved health outcomes, C17:0 produced negligible effects in preventing HF-diet induced health impairments.
The results presented herein demonstrate that the beneficial health outcomes associated with dairy intake are likely mediated through the effects of milk protein, while OCFA levels are likely a mere association and do not play a significant causal role in metabolic health under HF conditions. Furthermore, the highly divergent metabolic effects of the two BCAA, Leu and Val, unraveled herein highlight the importance of protein quality.
The doctoral thesis presented provides a comprehensive view of laser-based ablation techniques promoted to new fields of operation, including, but not limited to, size, composition, and concentration analyses. It covers various applications of laser ablation techniques over a wide range of sizes, from single molecules all the way to aerosol particles. The research for this thesis started with broadening and deepening the field of application and the fundamental understanding of liquid-phase IR-MALDI. Here, the hybridization of ion mobility spectrometry and microfluidics was realized by using IR-MALDI as the coupling technique for the first time. The setup was used for monitoring the photocatalytic performance of the E-Z isomerization of olefins. Using this hybrid, measurement times were so drastically reduced that such photocatalyst screenings became a matter of minutes rather than hours. With this on hand, triple measurements screenings could not only be performed within ten minutes, but also with a minimum amount of resources highlighting its potential as a green chemistry alternative to batch-sized reactions. Along the optimizing process of the IR-MALDI source for microfluidics came its application for another liquid sample supply method, the hanging drop. This demarcated one of the first applications of IR-MALDI for the charging of sub-micron particles directly from suspensions via their gas-phase transfer, followed by their characterization with differential mobility analysis. Given the high spectral quality of the data up to octuply charged particles became experimentally accessible, this laid the foundation for deriving a new charge distribution model for IR-MALDI in that size regime. Moving on to even larger analyte sizes, LIBS and LII were employed as ablation techniques for the solid phase, namely the aerosol particles themselves. Both techniques produce light-emitting events and were used to quantify and classify different aerosols. The unique configuration of stroboscopic imaging, photoacoustics, LII, and LIBS measurements opened new realms for analytical synergies and their potential application in industry. The concept of using low fluences, below 100 J/cm2, and high repetition rates of up to 500 Hz for LIBS makes for an excellent phase-selective LIBS setup. This concept was combined with a new approach to the photoacoustic normalization of LIBS. Also, it was possible to acquire statistically relevant amounts of data in a matter of seconds, showing its potential as a real-time optimization technique. On the same time axis, but at much lower fluences, LII was used with a similar methodology to quickly quantify and classify airborne particles of different compositions. For the first time, aerosol particles were evaluated on their LII susceptibility by using a fluence screening approach.
The complex hierarchical structure of bone undergoes a lifelong remodeling process, where it adapts to mechanical needs. Hereby, bone resorption by osteoclasts and bone formation by osteoblasts have to be balanced to sustain a healthy and stable organ. Osteocytes orchestrate this interplay by sensing mechanical strains and translating them into biochemical signals. The osteocytes are located in lacunae and are connected to one another and other bone cells via cell processes through small channels, the canaliculi. Lacunae and canaliculi form a network (LCN) of extracellular spaces that is able to transport ions and enables cell-to-cell communication. Osteocytes might also contribute to mineral homeostasis by direct interactions with the surrounding matrix. If the LCN is acting as a transport system, this should be reflected in the mineralization pattern. The central hypothesis of this thesis is that osteocytes are actively changing their material environment. Characterization methods of material science are used to achieve the aim of detecting traces of this interaction between osteocytes and the extracellular matrix. First, healthy murine bones were characterized. The properties analyzed were then compared with three murine model systems: 1) a loading model, where a bone of the mouse was loaded during its life time; 2) a healing model, where a bone of the mouse was cut to induce a healing response; and 3) a disease model, where the Fbn1 gene is dysfunctional causing defects in the formation of the extracellular tissue.
The measurement strategy included routines that make it possible to analyze the organization of the LCN and the material components (i.e., the organic collagen matrix and the mineral particles) in the same bone volumes and compare the spatial distribution of different data sets. The three-dimensional network architecture of the LCN is visualized by confocal laser scanning microscopy (CLSM) after rhodamine staining and is then subsequently quantified. The calcium content is determined via quantitative backscattered electron imaging (qBEI), while small- and wide-angle X-ray scattering (SAXS and WAXS) are employed to determine the thickness and length of local mineral particles.
First, tibiae cortices of healthy mice were characterized to investigate how changes in LCN architecture can be attributed to interactions of osteocytes with the surrounding bone matrix. The tibial mid-shaft cross-sections showed two main regions, consisting of a band with unordered LCN surrounded by a region with ordered LCN. The unordered region is a remnant of early bone formation and exhibited short and thin mineral particles. The surrounding, more aligned bone showed ordered and dense LCN as well as thicker and longer mineral particles. The calcium content was unchanged between the two regions.
In the mouse loading model, the left tibia underwent two weeks of mechanical stimulation, which results in increased bone formation and decreased resorption in skeletally mature mice. Here the specific research question addressed was how do bone material characteristics change at (re)modeling sites? The new bone formed in response to mechanical stimulation showed similar properties in terms of the mineral particles, like the ordered calcium region but lower calcium content compared to the right, non-loaded control bone of the same mice. There was a clear, recognizable border between mature and newly formed bone. Nevertheless, some canaliculi went through this border connecting the LCN of mature and newly formed bone.
Additionally, the question should be answered whether the LCN topology and the bone matrix material properties adapt to loading. Although, mechanically stimulated bones did not show differences in calcium content compared to controls, different correlations were found between the local LCN density and the local Ca content depending on whether the bone was loaded or not. These results suggest that the LCN may serve as a mineral reservoir.
For the healing model, the femurs of mice underwent an osteotomy, stabilized with an external fixator and were allowed to heal for 21 days. Thus, the spatial variations in the LCN topology with mineral properties within different tissue types and their interfaces, namely calcified cartilage, bony callus and cortex, could be simultaneously visualized and compared in this model. All tissue types showed structural differences across multiple length scales. Calcium content increased and became more homogeneous from calcified cartilage to bony callus to lamellar cortical bone. The degree of LCN organization increased as well, while the lacunae became smaller, as did the lacunar density between these different tissue types that make up the callus. In the calcified cartilage, the mineral particles were short and thin. The newly formed callus exhibited thicker mineral particles, which still had a low degree of orientation. While most of the callus had a woven-like structure, it also served as a scaffold for more lamellar tissue at the edges. The lamelar bone callus showed thinner mineral particles, but a higher degree of alignment in both, mineral particles and the LCN. The cortex showed the highest values for mineral length, thickness and degree of orientation. At the same time, the lacunae number density was 34% lower and the lacunar volume 40% smaller compared to bony callus. The transition zone between cortical and callus regions showed a continuous convergence of bone mineral properties and lacunae shape. Although only a few canaliculi connected callus and the cortical region, this indicates that communication between osteocytes of both tissues should be possible. The presented correlations between LCN architecture and mineral properties across tissue types may suggest that osteocytes have an active role in mineralization processes of healing.
A mouse model for the disease marfan syndrome, which includes a genetic defect in the fibrillin-1 gene, was investigated. In humans, Marfan syndrome is characterized by a range of clinical symptoms such as long bone overgrowth, loose joints, reduced bone mineral density, compromised bone microarchitecture, and increased fracture rates. Thus, fibrillin-1 seems to play a role in the skeletal homeostasis. Therefore, the present work studied how marfan syndrome alters LCN architecture and the surrounding bone matrix. The mice with marfan syndrome showed longer tibiae than their healthy littermates from an age of seven weeks onwards. In contrast, the cortical development appeared retarded, which was observed across all measured characteristics, i. e. lower endocortical bone formation, looser and less organized lacuno-canalicular network, less collagen orientation, thinner and shorter mineral particles.
In each of the three model systems, this study found that changes in the LCN architecture spatially correlated with bone matrix material parameters. While not knowing the exact mechanism, these results provide indications that osteocytes can actively manipulate a mineral reservoir located around the canaliculi to make a quickly accessible contribution to mineral homeostasis. However, this interaction is most likely not one-sided, but could be understood as an interplay between osteocytes and extra-cellular matrix, since the bone matrix contains biochemical signaling molecules (e.g. non-collagenous proteins) that can change osteocyte behavior. Bone (re)modeling can therefore not only be understood as a method for removing defects or adapting to external mechanical stimuli, but also for increasing the efficiency of possible osteocyte-mineral interactions during bone homeostasis. With these findings, it seems reasonable to consider osteocytes as a target for drug development related to bone diseases that cause changes in bone composition and mechanical properties. It will most likely require the combined effort of materials scientists, cell biologists, and molecular biologists to gain a deeper understanding of how bone cells respond to their material environment.
Two approaches for the synthesis of prenylated isoflavones were explored: the 2,3-oxidative rearrangement/cross metathesis approach, using hypervalent iodine reagents as oxidants and the Suzuki-Miyaura cross-coupling/cross metathesis approach. Three natural prenylated isoflavones: 5-deoxy-3′-prenylbiochanin A (59), erysubin F (61) and 7-methoxyebenosin (64), and non-natural analogues: 7,4′-dimethoxy-8,3′-diprenylisoflavone (126j) and 4′-hydroxy-7-methoxy-8,3′-diprenylisoflavone (128) were synthesized for the first time via the 2,3-oxidative rearrangement/cross metathesis approach, using mono- or diallylated flavanones as key intermediates. The reaction of flavanones with hypervalent iodine reagents afforded isoflavones via a 2,3-oxidative rearrangement and the corresponding flavone isomers via a 2,3-dehydrogenation. This afforded the synthesis of 7,4′-dimethoxy-8-prenylflavone (127g), 7,4′-dimethoxy-8,3′-diprenylflavone (127j), 7,4′-dihydroxy-8,3′-diprenylflavone (129) and 4′-hydroxy-7-methoxy-8,3′-diprenylflavone (130), the non-natural regioisomers of 7-methoxyebenosin, 126j, erysubin F and 128 respectively. Three natural prenylated isoflavones: 3′-prenylbiochanin A (58), neobavaisoflavone (66) and 7-methoxyneobavaisoflavone (137) were synthesized for the first time using the Suzuki-Miyaura cross-coupling/cross metathesis approach. The structures of 3′-prenylbiochanin A (58) and 5-deoxy-3′-prenylbiochanin A (59) were confirmed by single crystal X-ray diffraction analysis. The 2,3-oxidative rearrangement approach appears to be limited to the substitution pattern on both rings A and B of the flavanone while the Suzuki-Miyaura cross-coupling approach appears to be the most suitable for the synthesis of simple isoflavones or prenylated isoflavones whose prenyl substituents or allyl groups, the substituents that are essential precursors for the prenyl side chains, can be regioselectively introduced after the construction of the isoflavone core.
The chalcone-flavanone hybrids 146, 147 and 148, hybrids of the naturally occurring bioactive flavanones liquiritigenin-7-methyl ether, liquiritigenin and liquiritigenin-4′-methyl ether respectively were also synthesized for the first time, using Matsuda-Heck arylation and allylic/benzylic oxidation as key steps.
The intermolecular interactions of 5-deoxy-3′-prenylbiochanin A (59) and its two closely related precursors 106a and 106b was investigated by single crystal and Hirshfeld surface analyses to comprehend their different physicochemical properties. The results indicate that the presence of strong intermolecular O-H···O hydrogen bonds and an increase in the number of π-stacking interactions increases the melting point and lowers the solubility of isoflavone derivatives. However, the strong intermolecular O-H···O hydrogen bonds have a greater effect than the π-stacking interactions.
5-Deoxy-3′-prenylbiochanin A (59), erysubin F (61) and 7,4′-dihydroxy-8,3′-diprenylflavone (129), were tested against three bacterial strains and one fungal pathogen. All the three compounds were inactive against Salmonella enterica subsp. enterica (NCTC 13349), Escherichia coli (ATCC 25922), and Candida albicans (ATCC 90028), with MIC values greater than 80.0 μM. The diprenylated isoflavone erysubin F (61) and its flavone isomer 129 showed in vitro activity against methicillin-resistant Staphylococcus aureus (MRSA, ATCC 43300) at MIC values of 15.4 and 20.5 μM, respectively. 5-Deoxy-3′-prenylbiochanin A (59) was inactive against this MRSA strain. Erysubin F (61) and its flavone isomer 129 could serve as lead compounds for the development of new alternative drugs for the treatment of MRSA infections.
The ongoing climate change is altering the living conditions for many organisms on this planet at an unprecedented pace. Hence, it is crucial for the survival of species to adapt to these changing conditions. In this dissertation Silene vulgaris is used as a model organism to understand the adaption strategies of widely distributed plant species to the current climate change. Especially plant species that possess a wide geographic range are expected to have a high phenotypic plasticity or to show genetic differentiation in response to the different climate conditions they grow in. However, they are often underrepresented in research.
In the greenhouse experiment presented in this thesis, I examined the phenotypic responses and plasticity in S. vulgaris to estimate its’ adaptation potential. Seeds from 25 wild European populations were collected along a latitudinal gradient and grown in a greenhouse under three different precipitation (65 mm, 75 mm, 90 mm) and two different temperature regimes (18°C, 21°C) that resembled a possible climate change scenario for central Europe. Afterwards different biomass and fecundity-related plant traits were measured.
The treatments significantly influenced the plants but did not reveal a latitudinal difference in response to climate treatments for most plant traits. The number of flowers per individual however, showed a stronger plasticity in northern European populations (e.g., Swedish populations) where numbers decreased more drastically with increased temperature and decreased precipitation.
To gain an even deeper understanding of the adaptation of S. vulgaris to climate change it is also important to reveal the underlying phylogeny of the sampled populations. Therefore, I analysed their population genetic structure through whole genome sequencing via ddRAD.
The sequencing revealed three major genetic clusters in the S. vulgaris populations sampled in Europe: one cluster comprised Southern European populations, one cluster Western European populations and another cluster contained central European populations. A following analysis of experimental trait responses among the clusters to the climate-change scenario showed that the genetic clusters significantly differed in biomass-related traits and in the days to flowering. However, half of the traits showed parallel response patterns to the experimental climate-change scenario.
In addition to the potential geographic and genetic adaptation differences to climate change this dissertation also deals with the response differences between the sexes in S. vulgaris. As a gynodioecious species populations of S. vulgaris consist of female and hermaphrodite
individuals and the sexes can differ in their morphological traits which is known as sexual dimorphism. As climate change is becoming an important factor influencing plant morphology it remains unclear if and how different sexes may respond in sexually dimorphic species. To examine this question the sex of each individual plant was determined during the greenhouse experiment and the measured plant traits were analysed accordingly. In general, hermaphrodites had a higher number of flowers but a lower number of leaves than females. With regards to the climate change treatment, I found that hermaphrodites showed a milder negative response to higher temperatures in the number of flowers produced and in specific leaf area (SLA) compared to females.
Synthesis – The significant treatment response in Silene vulgaris, independent of population origin in most traits suggests a high degree of universal phenotypic plasticity. Also, the three European intraspecific genetic lineages detected showed comparable parallel response patterns in half of the traits suggesting considerable phenotypic plasticity. Hence, plasticity might represent a possible adaptation strategy of this widely distributed species during ongoing and future climatic changes. The results on sexual dimorphism show that females and hermaphrodites are differing mainly in their number of flowers and females are affected more strongly by the experimental climate-change scenario. These results provide a solid knowledge basis on the sexual dimorphism in S. vulgaris under climate change, but further research is needed to determine the long-term impact on the breeding system for the species.
In summary this dissertation provides a comprehensive insight into the adaptation mechanisms and consequences of a widely distributed and gynodioecious plant species and leverages our understanding of the impact of anthropogenic climate change on plants.
Proteine sind an praktisch allen Prozessen in lebenden Zellen maßgeblich beteiligt. Auch in der Biotechnologie werden Proteine in vielfältiger Weise eingesetzt.
Ein Protein besteht aus einer Kette von Aminosäuren. Häufig lagern sich mehrere dieser Ketten zu größeren Strukturen und Funktionseinheiten, sogenannten Proteinkomplexen,
zusammen. Kürzlich wurde gezeigt, dass eine Proteinkomplexbildung bereits während der Biosynthese der Proteine (co-translational) stattfinden kann
und nicht stets erst danach (post-translational) erfolgt. Da Fehlassemblierungen von Proteinen zu Funktionsverlusten und adversen Effekten führen, ist eine präzise und verlässliche Proteinkomplexbildung sowohl für zelluläre Prozesse als auch für biotechnologische Anwendungen essenziell. Mit experimentellen Methoden lassen sich zwar u.a. die Stöchiometrie und die Struktur von Proteinkomplexen bestimmen,
jedoch bisher nicht die Dynamik der Komplexbildung auf unterschiedlichen Zeitskalen. Daher sind grundlegende Mechanismen der Proteinkomplexbildung noch nicht vollständig verstanden. Die hier vorgestellte, auf experimentellen Erkenntnissen aufbauende, computergestützte Modellierung der Proteinkomplexbildung erlaubt eine umfassende Analyse des Einflusses physikalisch-chemischer Parameter
auf den Assemblierungsprozess. Die Modelle bilden möglichst realistisch die experimentellen Systeme der Kooperationspartner (Bar-Ziv, Weizmann-Institut, Israel; Bukau und Kramer, Universität Heidelberg) ab, um damit die Assemblierung von Proteinkomplexen einerseits in einem quasi-zweidimensionalen synthetischen Expressionssystem (in vitro) und andererseits im Bakterium Escherichia coli (in vivo) untersuchen zu können. Mit Hilfe eines vereinfachten Expressionssystems, in dem die Proteine nur an die Chip-Oberfläche, aber nicht aneinander binden können, wird das theoretische Modell parametrisiert. In diesem vereinfachten in-vitro-System durchläuft die Effizienz der Komplexbildung drei Regime – ein bindedominiertes Regime, ein Mischregime und ein produktionsdominiertes Regime. Ihr Maximum erreicht die Effizienz dabei kurz nach dem Übergang vom bindedominierten ins Mischregime und fällt anschließend monoton ab. Sowohl im nicht-vereinfachten in-vitro- als auch im in-vivo-System koexistieren je zwei konkurrierende Assemblierungspfade: Im in-vitro-System erfolgt die Komplexbildung entweder spontan in wässriger Lösung (Lösungsassemblierung) oder aber in einer definierten Schrittfolge an der Chip-Oberfläche (Oberflächenassemblierung); Im in-vivo-System konkurrieren hingegen die co- und die post-translationale Komplexbildung. Es zeigt sich, dass die Dominanz der Assemblierungspfade im in-vitro-System zeitabhängig ist und u.a. durch die Limitierung und Stärke der Bindestellen auf der Chip-Oberfläche beeinflusst werden kann. Im in-vivo-System hat der räumliche Abstand zwischen den Syntheseorten der beiden Proteinkomponenten nur dann einen Einfluss auf die Komplexbildung, wenn die Untereinheiten schnell degradieren. In diesem Fall dominiert die co-translationale Assemblierung auch auf kurzen Zeitskalen deutlich, wohingegen es bei stabilen Untereinheiten zu einem Wechsel von der Dominanz der post- hin zu einer geringen Dominanz der co-translationalen Assemblierung kommt. Mit den in-silico-Modellen lässt sich neben der Dynamik u.a. auch die Lokalisierung der Komplexbildung und -bindung darstellen, was einen Vergleich der theoretischen Vorhersagen mit experimentellen Daten und somit eine Validierung der Modelle ermöglicht. Der hier präsentierte in-silico Ansatz ergänzt die experimentellen Methoden, und erlaubt so, deren Ergebnisse zu interpretieren und neue Erkenntnisse davon abzuleiten.
Influenza A virus (IAV) is a pathogen responsible for severe seasonal epidemics threatening human and animal populations every year. During the viral assembly process in the infected cells, the plasma membrane (PM) has to bend in localized regions into a vesicle towards the extracellular side. Studies in cellular models have proposed that different viral proteins might be responsible for inducing membrane curvature in this context (including M1), but a clear consensus has not been reached. M1 is the most abundant protein in IAV particles. It plays an important role in virus assembly and budding at the PM. M1 is recruited to the host cell membrane where it associates with lipids and other viral proteins. However, the details of M1 interactions with the cellular PM, as well as M1-mediated membrane bending at the budozone, have not been clarified.
In this work, we used several experimental approaches to analyze M1-lipids and M1-M1 interactions. By performing SPR analysis, we quantified membrane association for full-length M1 and different genetically engineered M1 constructs (i.e., N- and C-terminally truncated constructs and a mutant of the polybasic region). This allowed us to obtain novel information on the protein regions mediating M1 binding to membranes. By using fluorescence microscopy, cryogenic transmission electron microscopy (cryo-TEM), and three-dimensional (3D) tomography (cryo-ET), we showed that M1 is indeed able to cause membrane deformation on vesicles containing negatively-charged lipids, in the absence of other viral components. Further, sFCS analysis proved that simple protein binding is not sufficient to induce membrane restructuring. Rather, it appears that stable M1-M1 interactions and multimer formation are required to alter the bilayer three-dimensional structure through the formation of a protein scaffold.
Finally, to mimic the budding mechanism in cells that arise by the lateral organization of the virus membrane components on lipid raft domains, we created vesicles with lipid domains. Our results showed that local binding of M1 to spatial confined acidic lipids within membrane domains of vesicles led to local M1 inward curvature.
Polymeric films and coatings derived from semi-crystalline oligomers are of relevance for medical and pharmaceutical applications. In this context, the material surface is of particular importance, as it mediates the interaction with the biological system. Two dimensional (2D) systems and ultrathin films are used to model this interface. However, conventional techniques for their preparation, such as spin coating or dip coating, have disadvantages, since the morphology and chain packing of the generated films can only be controlled to a limited extent and adsorption on the substrate used affects the behavior of the films. Detaching and transferring the films prepared by such techniques requires additional sacrificial or supporting layers, and free-standing or self supporting domains are usually of very limited lateral extension. The aim of this thesis is to study and modulate crystallization, melting, degradation and chemical reactions in ultrathin films of oligo(ε-caprolactone)s (OCL)s with different end-groups under ambient conditions. Here, oligomeric ultrathin films are assembled at the air-water interface using the Langmuir technique. The water surface allows lateral movement and aggregation of the oligomers, which, unlike solid substrates, enables dynamic physical and chemical interaction of the molecules. Parameters like surface pressure (π), temperature and mean molecular area (MMA) allow controlled assembly and manipulation of oligomer molecules when using the Langmuir technique. The π-MMA isotherms, Brewster angle microscopy (BAM), and interfacial infrared spectroscopy assist in detecting morphological and physicochemical changes in the film. Ultrathin films can be easily transferred to the solid silicon surface via Langmuir Schaefer (LS) method (horizontal substrate dipping). Here, the films transferred on silicon are investigated using atomic force microscopy (AFM) and optical microscopy and are compared to the films on the water surface.
The semi-crystalline morphology (lamellar thicknesses, crystal number densities, and lateral crystal dimensions) is tuned by the chemical structure of the OCL end-groups (hydroxy or methacrylate) and by the crystallization temperature (Tc; 12 or 21 °C) or MMAs. Compression to lower MMA of ~2 Å2, results in the formation of a highly crystalline film, which consists of tightly packed single crystals. Preparation of tightly packed single crystals on a cm2 scale is not possible by conventional techniques. Upon transfer to a solid surface, these films retain their crystalline morphology whereas amorphous films undergo dewetting.
The melting temperature (Tm) of OCL single crystals at the water and the solid surface is found proportional to the inverse crystal thickness and is generally lower than the Tm of bulk PCL. The impact of OCL end-groups on melting behavior is most noticeable at the air-solid interface, where the methacrylate end-capped OCL (OCDME) melted at lower temperatures than the hydroxy end-capped OCL (OCDOL). When comparing the underlying substrate, melting/recrystallization of OCL ultrathin films is possible at lower temperatures at the air water interface than at the air-solid interface, where recrystallization is not visible. Recrystallization at the air-water interface usually occurs at a higher temperature than the initial Tc.
Controlled degradation is crucial for the predictable performance of degradable polymeric biomaterials. Degradation of ultrathin films is carried out under acidic (pH ~ 1) or enzymatic catalysis (lipase from Pseudomonas cepcia) on the water surface or on a silicon surface as transferred films. A high crystallinity strongly reduces the hydrolytic but not the enzymatic degradation rate. As an influence of end-groups, the methacrylate end-capped linear oligomer, OCDME (~85 ± 2 % end-group functionalization) hydrolytically degrades faster than the hydroxy end capped linear oligomer, OCDOL (~95 ± 3 % end-group functionalization) at different temperatures. Differences in the acceleration of hydrolytic degradation of semi-crystalline films were observed upon complete melting, partial melting of the crystals, or by heating to temperatures close to Tm. Therefore, films of densely packed single crystals are suitable as barrier layers with thermally switchable degradation rates.
Chemical modification in ultrathin films is an intricate process applicable to connect functionalized molecules, impart stability or create stimuli-sensitive cross-links. The reaction of end-groups is explored for transferred single crystals on a solid surface or amorphous monolayer at the air-water interface. Bulky methacrylate end-groups are expelled to the crystal surface during chain-folded crystallization. The density of end-groups is inversely proportional to molecular weight and hence very pronounced for oligomers. The methacrylate end-groups at the crystal surface, which are present at high concentration, can be used for further chemical functionalization. This is demonstrated by fluorescence microscopy after reaction with fluorescein dimethacrylate. The thermoswitching behavior (melting and recrystallization) of fluorescein functionalized single crystals shows the temperature-dependent distribution of the chemically linked fluorescein moieties, which are accumulated on the surfaces of crystals, and homogeneously dispersed when the crystals are molten. In amorphous monolayers at the air-water interface, reversible cross-linking of hydroxy-terminated oligo(ε-caprolactone) monolayers using dialdehyde (glyoxal) lead to the formation of 2D networks. Pronounced contraction in the area occurred for 2D OCL films in dependence of surface pressure and time indicating the reaction progress. Cross linking inhibited crystallization and retarded enzymatic degradation of the OCL film. Altering the subphase pH to ~2 led to cleavage of the covalent acetal cross-links. Besides as model systems, these reversibly cross-linked films are applicable for drug delivery systems or cell substrates modulating adhesion at biointerfaces.